# Sepsis flow cytometry analysis

## Author: J.D. Hogan

### Overview

This project directory contains data, scripts, and output from the high dimensional flow cytometry analyses that were performed for the accompanying manuscript. Here is a brief description of each subdirectory within this project directory:

* `./bin/`: this subdirectory contains all of the R code used for the analyses presented in the manuscript
* `./data/`: this subdirectory contains input data used for the analyses, including .fcs files, metadata, panel information, and cluster merging information
* `./results/`: this subdirectory contains output from the analyses, including the R object daFrame and the results from GLM modeling on the data

### R version and libraries used

The code was developed for this manuscript using *R v4.1.1* and all packages called herein were installed in this version. The packages used for these analyses are (in alphabetical order, and what they're used for can be found as a comment in each library call in the scripts):

```
CATALYST
diffcyt
dplyr
flowCore
magrittr
SingleCellExperiment
```

### Running the code

To run the code for this project, make sure you are in the `./bin/` folder. To run the code that performs downsampling, clustering, and merging of the data, enter the command:

`Rscript ./run_flow_cyto_pipeline.R`

To run the code that performs statistical analysis of the cluster proportions, enter the command:

`Rscript ./stat_analysis.R`
